Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig

摘要

The roan coat color is characterized by white hairs intermingled with colored hairs. Candidate genes based on comparative phenotypes in horses and cattle involve the KIT and KIT ligand (MGF) genes. Here, we report the result of the whole genome scanning to detect genomic regions responsible for the roan coat color, using a three-generation pedigree of 62 pigs in an intercross between Landrace and Korean native pig. These pigs were genotyped using the PorcineSNP 60 BeadChip (Illumina, USA). The wholegenome scan indicated that three genomic regions, 35-36 Mb, 38-39 Mb, and 58-59 Mb on SSC8, were commonly and highly associated/linked with the roan phenotype in the case/control, sib-pair, and linkage test, respectively. The porcine KIT was selected asa candidate gene, because it is located in one of the three significant regions and its function is related to coat color formation. SNPs and hidels within coding sequence (CDS), promoter, and 3'-UTR of KIT were surveyed. Twenty-two SNPs in the CDS reported previously, as well as nine variations in promoter (2 SNPs) and 3'-UTR (5 SNPs and 2 Indels) were detected. Although no causative mutations were identified, these results will help to elucidate the genetic mechanisms involved in the expression of theroan phenotype and will aid in identifying key mutations responsible for the roan phenotype in further studies.